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Zhu Y, Mulholland MR, Bernhardt PW, Neeley AR, Widner B, Tapia AM, Echevarria MA. Nitrogen uptake rates and phytoplankton composition across contrasting North Atlantic Ocean coastal regimes north and south of Cape Hatteras. Front Microbiol 2024; 15:1380179. [PMID: 38784802 PMCID: PMC11113559 DOI: 10.3389/fmicb.2024.1380179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
Understanding nitrogen (N) uptake rates respect to nutrient availability and the biogeography of phytoplankton communities is crucial for untangling the complexities of marine ecosystems and the physical, biological, and chemical forces shaping them. In the summer of 2016, we conducted measurements of bulk microbial uptake rates for six 15N-labeled substrates: nitrate, nitrite, ammonium, urea, cyanate, and dissolve free amino acids across distinct marine provinces, including the continental shelf of the Mid-and South Atlantic Bights (MAB and SAB), the Slope Sea, and the Gulf Stream, marking the first instance of simultaneously measuring six different N uptake rates in this dynamic region. Total measured N uptake rates were lowest in the Gulf Stream followed by the SAB. Notably, the MAB exhibited significantly higher N uptake rates compared to the SAB, likely due to the excess levels of pre-existing phosphorus present in the MAB. Together, urea and nitrate uptake contributed approximately 50% of the total N uptake across the study region. Although cyanate uptake rates were consistently low, they accounted for up to 11% of the total measured N uptake at some Gulf Stream stations. Phytoplankton groups were identified based on specific pigment markers, revealing a dominance of diatoms in the shelf community, while Synechococcus, Prochlorococcus, and pico-eukaryotes dominated in oligotrophic Gulf Stream waters. The reported uptake rates in this study were mostly in agreement with previous studies conducted in coastal waters of the North Atlantic Ocean. This study suggests there are distinct regional patterns of N uptake in this physically dynamic region, correlating with nutrient availability and phytoplankton community composition. These findings contribute valuable insights into the intricate interplay of biological and chemical factors shaping N dynamics in disparate marine ecosystems.
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Affiliation(s)
- Yifan Zhu
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Margaret R. Mulholland
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
| | - Peter W. Bernhardt
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
| | | | - Brittany Widner
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
| | - Alfonso Macías Tapia
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
- Office of Education, National Oceanic and Atmospheric Administration, Silver Spring, MD, United States
| | - Michael A. Echevarria
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, United States
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2
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Kiledal EA, Reitz LA, Kuiper EQ, Evans J, Siddiqui R, Denef VJ, Dick GJ. Comparative genomic analysis of Microcystis strain diversity using conserved marker genes. HARMFUL ALGAE 2024; 132:102580. [PMID: 38331539 DOI: 10.1016/j.hal.2024.102580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/10/2024]
Abstract
Microcystis-dominated cyanobacterial harmful algal blooms (cyanoHABs) have a global impact on freshwater environments, affecting both wildlife and human health. Microcystis diversity and function in field samples and laboratory cultures can be determined by sequencing whole genomes of cultured isolates or natural populations, but these methods remain computationally and financially expensive. Amplicon sequencing of marker genes is a lower cost and higher throughput alternative to characterize strain composition and diversity in mixed samples. However, the selection of appropriate marker gene region(s) and primers requires prior understanding of the relationship between single gene genotype, whole genome content, and phenotype. To identify phylogenetic markers of Microcystis strain diversity, we compared phylogenetic trees built from each of 2,351 individual core genes to an established phylogeny and assessed the ability of these core genes to predict whole genome content and bioactive compound genotypes. We identified single-copy core genes better able to resolve Microcystis phylogenies than previously identified marker genes. We developed primers suitable for current Illumina-based amplicon sequencing with near-complete coverage of available Microcystis genomes and demonstrate that they outperform existing options for assessing Microcystis strain composition. Results showed that genetic markers can be used to infer Microcystis gene content and phenotypes such as potential production of bioactive compounds , although marker performance varies by bioactive compound gene and sequence similarity. Finally, we demonstrate that these markers can be used to characterize the Microcystis strain composition of laboratory or field samples like those collected for surveillance and modeling of Microcystis-dominated cyanobacterial harmful algal blooms.
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Affiliation(s)
- E Anders Kiledal
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA.
| | - Laura A Reitz
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA
| | - Esmée Q Kuiper
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA
| | - Jacob Evans
- Department of Ecology and Evolutionary Biology, University of Michigan, 2220 Biological Sciences Building, 1105 North University Avenue, Ann Arbor, MI 48109-1005, USA
| | - Ruqaiya Siddiqui
- Microbiome Core, University of Michigan, 1500 MSRB 1, 1150W Medical Center Drive, Ann Arbor, MI 48109-5666, USA
| | - Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, 2220 Biological Sciences Building, 1105 North University Avenue, Ann Arbor, MI 48109-1005, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA; Cooperative Institute for Great Lakes Research, University of Michigan, 4040 Dana Building, 440 Church Street, Ann Arbor, MI 48109-1041, USA
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Díez J, López-Lozano A, Domínguez-Martín MA, Gómez-Baena G, Muñoz-Marín MC, Melero-Rubio Y, García-Fernández JM. Regulatory and metabolic adaptations in the nitrogen assimilation of marine picocyanobacteria. FEMS Microbiol Rev 2023; 47:6794272. [PMID: 36323406 DOI: 10.1093/femsre/fuac043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Prochlorococcus and Synechococcus are the two most abundant photosynthetic organisms on Earth, with a strong influence on the biogeochemical carbon and nitrogen cycles. Early reports demonstrated the streamlining of regulatory mechanisms in nitrogen metabolism and the removal of genes not strictly essential. The availability of a large series of genomes, and the utilization of latest generation molecular techniques have allowed elucidating the main mechanisms developed by marine picocyanobacteria to adapt to the environments where they thrive, with a particular interest in the strains inhabiting oligotrophic oceans. Given that nitrogen is often limited in those environments, a series of studies have explored the strategies utilized by Prochlorococcus and Synechococcus to exploit the low concentrations of nitrogen-containing molecules available in large areas of the oceans. These strategies include the reduction in the GC and the cellular protein contents; the utilization of truncated proteins; a reduced average amount of N in the proteome; the development of metabolic mechanisms to perceive and utilize nanomolar nitrate concentrations; and the reduced responsiveness of key molecular regulatory systems such as NtcA to 2-oxoglutarate. These findings are in sharp contrast with the large body of knowledge obtained in freshwater cyanobacteria. We will outline the main discoveries, stressing their relevance to the ecological success of these important microorganisms.
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Affiliation(s)
- J Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - A López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M A Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - G Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M C Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - Y Melero-Rubio
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - J M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
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Yang N, Lin YA, Merkel CA, DeMers MA, Qu PP, Webb EA, Fu FX, Hutchins DA. Molecular mechanisms underlying iron and phosphorus co-limitation responses in the nitrogen-fixing cyanobacterium Crocosphaera. THE ISME JOURNAL 2022; 16:2702-2711. [PMID: 36008474 PMCID: PMC9666452 DOI: 10.1038/s41396-022-01307-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
In the nitrogen-limited subtropical gyres, diazotrophic cyanobacteria, including Crocosphaera, provide an essential ecosystem service by converting dinitrogen (N2) gas into ammonia to support primary production in these oligotrophic regimes. Natural gradients of phosphorus (P) and iron (Fe) availability in the low-latitude oceans constrain the biogeography and activity of diazotrophs with important implications for marine biogeochemical cycling. Much remains unknown regarding Crocosphaera's physiological and molecular responses to multiple nutrient limitations. We cultured C. watsonii under Fe, P, and Fe/P (co)-limiting scenarios to link cellular physiology with diel gene expression and observed unique physiological and transcriptional profiles for each treatment. Counterintuitively, reduced growth and N2 fixation resource use efficiencies (RUEs) for Fe or P under P limitation were alleviated under Fe/P co-limitation. Differential gene expression analyses show that Fe/P co-limited cells employ the same responses as single-nutrient limited cells that reduce cellular nutrient requirements and increase responsiveness to environmental change including smaller cell size, protein turnover (Fe-limited), and upregulation of environmental sense-and-respond systems (P-limited). Combined, these mechanisms enhance growth and RUEs in Fe/P co-limited cells. These findings are important to our understanding of nutrient controls on N2 fixation and the implications for primary productivity and microbial dynamics in a changing ocean.
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Affiliation(s)
- Nina Yang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yu-An Lin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Carlin A Merkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michelle A DeMers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ping-Ping Qu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric A Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fei-Xue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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Domínguez-Martín MA, López-Lozano A, Melero-Rubio Y, Gómez-Baena G, Jiménez-Estrada JA, Kukil K, Diez J, García-Fernández JM. Marine Synechococcus sp. Strain WH7803 Shows Specific Adaptative Responses to Assimilate Nanomolar Concentrations of Nitrate. Microbiol Spectr 2022; 10:e0018722. [PMID: 35852322 PMCID: PMC9430850 DOI: 10.1128/spectrum.00187-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022] Open
Abstract
Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrient availability and temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to micromolar ammonium or nitrogen starvation. We found that Synechococcus has a specific response to a nanomolar nitrate concentration that differs from the response shown under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentrations of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural environment. IMPORTANCE Marine Synechococcus are a very abundant group of photosynthetic organisms on our planet. Previous studies have shown blooms of these organisms when nanomolar concentrations of nitrate become available. We have assessed the effect of nanomolar nitrate concentrations by studying the transcriptome and proteome of Synechococcus sp. WH7803, together with some physiological parameters. We found evidence that Synechococcus sp. strain WH7803 does sense and react to nanomolar concentrations of nitrate, suggesting the occurrence of specific adaptive mechanisms to allow their utilization. Thus, very low concentrations of nitrate in the ocean seem to be a significant nitrogen source for marine picocyanobacteria.
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Grants
- Ministerio de Ciencia e Innovacion, Government of Spain (cofunded by the FEDER program, European Union)
- Consejeria de Conocimiento, Investigacion y Universidad, Junta de Andalucia (Spain), cofunded by the FEDER program (European Union)
- Universidad de Cordoba (Spain), Programa Propio de Investigacion
- Junta de Andalucia (Spain), Programa Operativo de Empleo Juvenil, cofunded by the FEDER programme (European Union)
- Consejería de Transformación Económica, Industria, Conocimiento y Universidades, Junta de Andalucia (Spain), cofunded by the FEDER program (European Union)
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Affiliation(s)
- María Agustina Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Yesica Melero-Rubio
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Juan Andrés Jiménez-Estrada
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Kateryna Kukil
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Jesús Diez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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Distribution and Environmental Impact Factors of Picophytoplankton in the Eastern Indian Ocean. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10050628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Picophytoplankton (pico) in the eastern Indian Ocean (EIO) were investigated during the inter-monsoon periods. They were found to typically comprise Prochlorococcus (Pro), Synechococcus (Syn), and Picoeukaryotes (PEuks). In the survey area, the pico showed two different vertical distribution patterns in different regions, whereby the Syn abundance decreased with depth, whereas those of Pro and PEuks increased and then decreased with depth, with the maximum depths ranging from 50 to 100 m. The cell abundance and community structure of the pico were similar at the equator (EQ) and the eastern boundary of the Indian Ocean near Sumatra (EB), but the pico cell abundance was significantly lower in the Bay of Bengal (BOB). Pro dominated most regions of the entire EIO and were approximately one-to-two orders of magnitude more abundant than Syn and PEuks. The distributions of Syn and PEuks showed little difference across various regions. Influenced by the physicochemistry of circulation and water masses, there were many different environmental factors in the different regions. The abundance of pico domination by Pro showed a strong positive correlation with the nutrients and salinity in the survey area, indicating increasing nutrient availability, particularly in the oligotrophic EIO. Generalized additive models (GAMs) analysis showed the differences in their responses to environmental variability. Pro and PEuks both increased strongly with warming up to below 26 °C, and Pro and PEuks were more responsive to chemical (nutrient) variability. Syn showed a broader tolerance of low-salinity conditions. In a certain range, an increase in nitrite and nitric acid can improve the cell abundance of Pro. As a significant contributor to primary productivity in oligotrophic waters, this study provides essential information for studying pico communities in the EIO and its adjacent marine ecosystems.
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Proteome Expression and Survival Strategies of a Proteorhodopsin-Containing Vibrio Strain under Carbon and Nitrogen Limitation. mSystems 2022; 7:e0126321. [PMID: 35384695 PMCID: PMC9040609 DOI: 10.1128/msystems.01263-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Photoheterotrophy is a widespread mode of microbial metabolism, notably in the oligotrophic surface ocean, where microbes experience chronic nutrient limitation. One especially widespread form of photoheterotrophy is based on proteorhodopsin (PR), which uses light to generate proton motive force that can drive ATP synthesis, flagellar movement, or nutrient uptake. To clarify the physiological benefits conferred by PR under nutrient stress conditions, we quantified protein-level gene expression of Vibrio campbellii CAIM 519 under both carbon and nitrogen limitation and under both light and dark conditions. Using a novel membrane proteomics strategy, we determined that PR expression is higher under C limitation than N limitation but is not light regulated. Despite expression of PR photosystems, V. campbellii does not exhibit any growth or survival advantages in the light and only a few proteins show significant expression differences between light and dark conditions. While protein-level proteorhodopsin expression in V. campbellii is clearly responsive to nutrient limitation, photoheterotrophy does not appear to play a central role in the survival physiology of this organism under these nutrient stress conditions. C limitation and N limitation, however, result in very different survival responses: under N-limited conditions, viability declines, cultivability is lost rapidly, central carbon flux through the Entner-Doudoroff pathway is increased, and ammonium is assimilated via the GS-GOGAT pathway. In contrast, C limitation drives cell dwarfing with maintenance of viability, as well as utilization of the glyoxylate shunt, glutamate dehydrogenase and anaplerotic C fixation, and a stringent response mediated by the Pho regulon. IMPORTANCE Understanding the nutrient stress responses of proteorhodopsin-bearing microbes like Vibrio campbellii yields insights into microbial contributions to nutrient cycling, lifestyles of emerging pathogens in aquatic environments, and protein-level adaptations implemented during times of nutrient limitation. In addition to its broad taxonomic and geographic prevalence, the physiological role of PR is diverse, so we developed a novel proteomics strategy to quantify its expression at the protein level. We found that proteorhodopsin expression levels in this wild-type photoheterotroph under these experimental conditions, while higher under C than under N limitation, do not afford measurable light-driven growth or survival advantages. Additionally, this work links differential protein expression patterns between C- and N-limited cultures to divergent stationary-phase survival phenotypes.
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Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages. THE ISME JOURNAL 2022; 16:488-499. [PMID: 34429521 PMCID: PMC8776855 DOI: 10.1038/s41396-021-01085-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/07/2023]
Abstract
Marine cyanobacteria of the genera Synechococcus and Prochlorococcus are the most abundant photosynthetic organisms on earth, spanning vast regions of the oceans and contributing significantly to global primary production. Their viruses (cyanophages) greatly influence cyanobacterial ecology and evolution. Although many cyanophage genomes have been sequenced, insight into the functional role of cyanophage genes is limited by the lack of a cyanophage genetic engineering system. Here, we describe a simple, generalizable method for genetic engineering of cyanophages from multiple families, that we named REEP for REcombination, Enrichment and PCR screening. This method enables direct investigation of key cyanophage genes, and its simplicity makes it adaptable to other ecologically relevant host-virus systems. T7-like cyanophages often carry integrase genes and attachment sites, yet exhibit lytic infection dynamics. Here, using REEP, we investigated their ability to integrate and maintain a lysogenic life cycle. We found that these cyanophages integrate into the host genome and that the integrase and attachment site are required for integration. However, stable lysogens did not form. The frequency of integration was found to be low in both lab cultures and the oceans. These findings suggest that T7-like cyanophage integration is transient and is not part of a classical lysogenic cycle.
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Walworth NG, Saito MA, Lee MD, McIlvin MR, Moran DM, Kellogg RM, Fu FX, Hutchins DA, Webb EA. Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium. J Proteome Res 2021; 21:77-89. [PMID: 34855411 DOI: 10.1021/acs.jproteome.1c00517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ocean microbial communities are important contributors to the global biogeochemical reactions that sustain life on Earth. The factors controlling these communities are being increasingly explored using metatranscriptomic and metaproteomic environmental biomarkers. Using published proteomes and transcriptomes from the abundant colony-forming cyanobacterium Trichodesmium (strain IMS101) grown under varying Fe and/or P limitation in low and high CO2, we observed robust correlations of stress-induced proteins and RNAs (i.e., involved in transport and homeostasis) that yield useful information on the nutrient status under low and/or high CO2. Conversely, transcriptional and translational correlations of many other central metabolism pathways exhibit broad discordance. A cellular RNA and protein production/degradation model demonstrates how biomolecules with small initial inventories, such as environmentally responsive proteins, achieve large increases in fold-change units as opposed to those with a higher basal expression and inventory such as metabolic systems. Microbial cells, due to their immersion in the environment, tend to show large adaptive responses in both RNA and protein that result in transcript-protein correlations. These observations and model results demonstrate multi-omic coherence for environmental biomarkers and provide the underlying mechanism for those observations, supporting the promise for global application in detecting responses to environmental stimuli in a changing ocean.
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Affiliation(s)
- Nathan G Walworth
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, Washington 98104, United States.,Exobiology Branch, NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Matthew R McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Dawn M Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Riss M Kellogg
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Fei-Xue Fu
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Eric A Webb
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
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10
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Ma J, Song J, Li X, Wang Q, Sun X, Zhang W, Zhong G. Seawater stratification vs. plankton for oligotrophic mechanism: A case study of M4 seamount area in the Western Pacific Ocean. MARINE ENVIRONMENTAL RESEARCH 2021; 169:105400. [PMID: 34186434 DOI: 10.1016/j.marenvres.2021.105400] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Oligotrophic sea area mainly distributes in tropical and subtropical ocean, which have a profound impact on the marine material cycle and the structure of biological community. Based on the comprehensive survey in M4 seamount area of the Tropical Western Pacific Ocean in August 2017, the nutrients characteristics were explained, the formation mechanism of oligotrophic characteristics in this region was explored, and the influence of M4 seamount on oligotrophic sea area was analyzed. The results showed that the M4 seamount area is a typical oligotrophic sea area. In the water column of 0-100 m, the nutrients levels are extremely low, and NO3-N, PO4-P and SiO3-Si are lower than 0.55, 0.15 and 1.75 μmol/L, respectively; in the water column of 100-500 m, the nutrients concentrations rise rapidly, forming nutriclines. Seawater stratification is one of the main reasons for the formation of oligotrophic characteristics in this area. The thermocline in the water column of 100-500 m and the high-salt area in the water column of 100-230 m form a dual effect, which hinders the upward transport of waters with high nutrients concentrations at the bottom. In addition, Synechococcus and bacteria grow and multiply in a large amount in the water column of 0-100 m, absorb and utilize nutrients, and aggravate the oligotrophic characteristics of this area. There are significant upwellings near the summit of the M4 seamount, which promotes the waters with high nutrients concentrations at the bottom to break through the barriers of the thermocline and high-salt area and to transport upwards into the euphotic layer, which can be better utilized by phytoplankton. This study showed that seamounts may have an important effect on improving the oligotrophic characteristics of local sea areas, and then promote the growth of phytoplankton.
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Affiliation(s)
- Jun Ma
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jinming Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Xuegang Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Qidong Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xiaoxia Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Wuchang Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Guorong Zhong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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11
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Mine AH, Coleman ML, Colman AS. Phosphorus Release and Regeneration Following Laboratory Lysis of Bacterial Cells. Front Microbiol 2021; 12:641700. [PMID: 33897649 PMCID: PMC8060472 DOI: 10.3389/fmicb.2021.641700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/10/2021] [Indexed: 11/30/2022] Open
Abstract
The availability of phosphorus limits primary production in large regions of the oceans, and marine microbes use a variety of strategies to overcome this limitation. One strategy is the production of alkaline phosphatase (APase), which allows hydrolysis of larger dissolved organic phosphorus (DOP) compounds in the periplasm or at the cell surface for transport of orthophosphate into the cell. Cell lysis, driven by grazing and viral infection, releases phosphorus-containing cell components, along with active enzymes that could persist after lysis. The importance of this continued enzymatic activity for orthophosphate regeneration is unknown. We used three model bacteria – Escherichia coli K-12 MG1655, Synechococcus sp. WH7803, and Prochlorococcus sp. MED4 – to assess the impact of continued APase activity after cell lysis, via lysozyme treatment, on orthophosphate regeneration. Direct release of orthophosphate scaled with cell size and was reduced under phosphate-starved conditions where APase activity continued for days after lysis. All lysate incubations showed post-lysis orthophosphate generation suggesting phosphatases other than APase maintain activity. Rates of DOP hydrolysis and orthophosphate remineralization varied post-lysis among strains. Escherichia coli K-12 MG1655 rates of remineralization were 0.6 and 1.2 amol cell–1hr–1 under deplete and replete conditions; Synechococcus WH7803 lysates ranged from 0.04 up to 0.3 amol cell–1hr–1 during phosphorus deplete and replete conditions, respectively, while in Prochlorococcus MED4 lysates, rates were stable at 0.001 amol cell–1hr–1 in both conditions. The range of rates of hydrolysis and regeneration underscores the taxonomic and biochemical variability in the process of nutrient regeneration and further highlights the complexity of quantitatively resolving the major fluxes within the microbial loop.
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Affiliation(s)
- Aric H Mine
- Department of Earth and Environmental Sciences, California State University, Fresno, CA, United States.,Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Albert S Colman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States.,Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, TX, United States
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12
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Gomes Gradíssimo D, Pereira Xavier L, Valadares Santos A. Cyanobacterial Polyhydroxyalkanoates: A Sustainable Alternative in Circular Economy. Molecules 2020; 25:E4331. [PMID: 32971731 PMCID: PMC7571216 DOI: 10.3390/molecules25184331] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 01/11/2023] Open
Abstract
Conventional petrochemical plastics have become a serious environmental problem. Its unbridled use, especially in non-durable goods, has generated an accumulation of waste that is difficult to measure, threatening aquatic and terrestrial ecosystems. The replacement of these plastics with cleaner alternatives, such as polyhydroxyalkanoates (PHA), can only be achieved by cost reductions in the production of microbial bioplastics, in order to compete with the very low costs of fossil fuel plastics. The biggest costs are carbon sources and nutrients, which can be appeased with the use of photosynthetic organisms, such as cyanobacteria, that have a minimum requirement for nutrients, and also using agro-industrial waste, such as the livestock industry, which in turn benefits from the by-products of PHA biotechnological production, for example pigments and nutrients. Circular economy can help solve the current problems in the search for a sustainable production of bioplastic: reducing production costs, reusing waste, mitigating CO2, promoting bioremediation and making better use of cyanobacteria metabolites in different industries.
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Affiliation(s)
- Diana Gomes Gradíssimo
- Post Graduation Program in Biotechnology, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil;
| | - Luciana Pereira Xavier
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil;
| | - Agenor Valadares Santos
- Post Graduation Program in Biotechnology, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil;
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13
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Shilova IN, Magasin JD, Mills MM, Robidart JC, Turk-Kubo KA, Zehr JP. Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system. PLoS One 2020; 15:e0231771. [PMID: 32310982 PMCID: PMC7170224 DOI: 10.1371/journal.pone.0231771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/31/2020] [Indexed: 11/18/2022] Open
Abstract
Marine phytoplankton are responsible for approximately half of photosynthesis on Earth. However, their ability to drive ocean productivity depends on critical nutrients, especially bioavailable nitrogen (N) which is scarce over vast areas of the ocean. Phytoplankton differ in their preferences for N substrates as well as uptake efficiencies and minimal N requirements relative to other critical nutrients, including iron (Fe) and phosphorus. In this study, we used the MicroTOOLs high-resolution environmental microarray to examine transcriptomic responses of phytoplankton communities in the California Current System (CCS) transition zone to added urea, ammonium, nitrate, and also Fe in the late summer when N depletion is common. Transcript level changes of photosynthetic, carbon fixation, and nutrient stress genes indicated relief of N limitation in many strains of Prochlorococcus, Synechococcus, and eukaryotic phytoplankton. The transcriptomic responses helped explain shifts in physiological and growth responses observed later. All three phytoplankton groups had increased transcript levels of photosynthesis and/or carbon fixation genes in response to all N substrates. However, only Prochlorococcus had decreased transcript levels of N stress genes and grew substantially, specifically after urea and ammonium additions, suggesting that Prochlorococcus outcompeted other community members in these treatments. Diatom transcript levels of carbon fixation genes increased in response to Fe but not to Fe with N which might have favored phytoplankton that were co-limited by N and Fe. Moreover, transcription patterns of closely related strains indicated variability in N utilization, including nitrate utilization by some high-light adapted Prochlorococcus. Finally, up-regulation of urea transporter genes by both Prochlorococcus and Synechococcus in response to filtered deep water suggested a regulatory mechanism other than classic control via the global N regulator NtcA. This study indicated that co-existing phytoplankton strains experience distinct nutrient stresses in the transition zone of the CCS, an understudied region where oligotrophic and coastal communities naturally mix.
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Affiliation(s)
- Irina N. Shilova
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (INS); (JPZ)
| | - Jonathan D. Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Matthew M. Mills
- Department of Earth System Science, Stanford University, Stanford, California, United States of America
| | - Julie C. Robidart
- Ocean Technology and Engineering, National Oceanography Centre, Southampton, England, United Kingdom
| | - Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (INS); (JPZ)
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14
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Resistance in marine cyanobacteria differs against specialist and generalist cyanophages. Proc Natl Acad Sci U S A 2019; 116:16899-16908. [PMID: 31383764 PMCID: PMC6708340 DOI: 10.1073/pnas.1906897116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Long-term coexistence between unicellular cyanobacteria and their lytic viruses (cyanophages) in the oceans is thought to be due to the presence of sensitive cells in which cyanophages reproduce, ultimately killing the cell, while other cyanobacteria survive due to resistance to infection. Here, we investigated resistance in marine cyanobacteria from the genera Synechococcus and Prochlorococcus and compared modes of resistance against specialist and generalist cyanophages belonging to the T7-like and T4-like cyanophage families. Resistance was extracellular in most interactions against specialist cyanophages irrespective of the phage family, preventing entry into the cell. In contrast, resistance was intracellular in practically all interactions against generalist T4-like cyanophages. The stage of intracellular arrest was interaction-specific, halting at various stages of the infection cycle. Incomplete infection cycles proceeded to various degrees of phage genome transcription and translation as well as phage genome replication in numerous interactions. In a particularly intriguing case, intracellular capsid assembly was observed, but the phage genome was not packaged. The cyanobacteria survived the encounter despite late-stage infection and partial genome degradation. We hypothesize that this is tolerated due to genome polyploidy, which we found for certain strains of both Synechococcus and Prochlorococcus Our findings unveil a heavy cost of promiscuous entry of generalist phages into nonhost cells that is rarely paid by specialist phages and suggests the presence of unknown mechanisms of intracellular resistance in the marine unicellular cyanobacteria. Furthermore, these findings indicate that the range for virus-mediated horizontal gene transfer extends beyond hosts to nonhost cyanobacterial cells.
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15
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Enav H, Kirzner S, Lindell D, Mandel-Gutfreund Y, Béjà O. Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean. Nat Commun 2018; 9:4698. [PMID: 30409965 PMCID: PMC6224464 DOI: 10.1038/s41467-018-07164-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/22/2018] [Indexed: 12/16/2022] Open
Abstract
Cyanophages of the Myoviridae family include generalist viruses capable of infecting a wide range of hosts including those from different cyanobacterial genera. While the influence of phages on host evolution has been studied previously, it is not known how the infection of distinct hosts influences the evolution of cyanophage populations. Here, using an experimental evolution approach, we investigated the adaptation of multiple cyanophage populations to distinct cyanobacterial hosts. We show that when infecting an "optimal" host, whose infection is the most efficient, phage populations accumulated only a few mutations. However, when infecting "sub-optimal" hosts, different mutations spread in the phage populations, leading to rapid diversification into distinct subpopulations. Based on our results, we propose a model demonstrating how shifts in microbial abundance, which lead to infection of "sub-optimal" hosts, act as a driver for rapid diversification of viral populations.
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Affiliation(s)
- Hagay Enav
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel. .,Department of Microbiome Science, Max-Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
| | - Shay Kirzner
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Debbie Lindell
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.,Department of Computer Sciences, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
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16
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Ma X, Coleman ML, Waldbauer JR. Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria. Environ Microbiol 2018; 20:3001-3011. [PMID: 30047191 DOI: 10.1111/1462-2920.14338] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 11/29/2022]
Abstract
Dissolved organic matter (DOM) plays a central role in the microbial ecology and biogeochemistry of aquatic environments, yet little is known about how the mechanism of DOM release from its ultimate source, primary producer biomass, affects the molecular composition of the inputs to the dissolved pool. Here we used a model marine phytoplankton, the picocyanobacterium Synechococcus WH7803, to compare the composition of DOM released by three mechanisms: exudation, mechanical cell lysis and infection by the lytic phage S-SM1. A broad, untargeted analytical approach reveals the complexity of this freshly sourced DOM, and comparative analysis between DOM produced by the different mechanisms suggests that exudation and viral lysis are sources of unsaturated, oxygen-rich and possibly novel biomolecules. Furthermore, viral lysis of WH7803 by S-SM1 releases abundant peptides derived from specific proteolysis of the major light-harvesting protein phycoerythrin, raising the possibility that phage infection of these abundant cyanobacteria could be a significant source of high molecular weight dissolved organic nitrogen compounds.
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Affiliation(s)
- Xiufeng Ma
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
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17
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Barón-Sola Á, Fernández Del Campo F, Sanz-Alférez S. Influence of Glycine and Arginine on Cylindrospermopsin Production and aoa Gene Expression in Aphanizomenon ovalisporum. Toxins (Basel) 2017; 9:toxins9110355. [PMID: 29104251 PMCID: PMC5705970 DOI: 10.3390/toxins9110355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 10/24/2017] [Accepted: 10/26/2017] [Indexed: 11/16/2022] Open
Abstract
Arginine (Arg) and glycine (Gly) seem to be the only substrates accepted by the amidinotransferase that catalyze the first step of the synthesis pathway of the cyanotoxin cylindrospermopsin (CYN), leading to guanidinoacetate (GAA). Here, the effect of these amino acids on the production of CYN in cultures of the cylindrospermopsin-producing strain, Aphanizomenon ovalisporum UAM-MAO, has been studied. Arg clearly increased CYN content, the increment appearing triphasic along the culture. On the contrary, Gly caused a decrease of CYN, observable from the first day on. Interestingly, the transcript of the gene ntcA, key in nitrogen metabolism control, was also enhanced in the presence of Arg and/or Gly, the trend of the transcript oscillations being like that of aoa/cyr. The inhibitory effect of Gly in CYN production seems not to result from diminishing the activity of genes considered involved in CYN synthesis, since Gly, as Arg, enhance the transcription of genes aoaA-C and cyrJ. On the other hand, culture growth is affected by Arg and Gly in a similar way to CYN production, with Arg stimulating and Gly impairing it. Taken together, our data show that the influence of both Arg and Gly on CYN changes seems not to be due to a specific effect on the first step of CYN synthesis; it rather appears to be the result of changes in the physiological cell status.
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Affiliation(s)
- Ángel Barón-Sola
- Departament of Biology, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain.
| | | | - Soledad Sanz-Alférez
- Departament of Biology, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain.
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18
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Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function. ISME JOURNAL 2017; 12:343-355. [PMID: 29028002 PMCID: PMC5776448 DOI: 10.1038/ismej.2017.159] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 08/17/2017] [Accepted: 08/22/2017] [Indexed: 11/08/2022]
Abstract
Cyanobacteria are among the most abundant photosynthetic organisms in the oceans; viruses infecting cyanobacteria (cyanophages) can alter cyanobacterial populations, and therefore affect the local food web and global biochemical cycles. These phages carry auxiliary metabolic genes (AMGs), which rewire various metabolic pathways in the infected host cell, resulting in increased phage fitness. Coping with stress resulting from photodamage appears to be a central necessity of cyanophages, yet the overall mechanism is poorly understood. Here we report a novel, widespread cyanophage AMG, encoding a fatty acid desaturase (FAD), found in two genotypes with distinct geographical distribution. FADs are capable of modulating the fluidity of the host’s membrane, a fundamental stress response in living cells. We show that both viral FAD (vFAD) families are Δ9 lipid desaturases, catalyzing the desaturation at carbon 9 in C16 fatty acid chains. In addition, we present a comprehensive fatty acid profiling for marine cyanobacteria, which suggests a unique desaturation pathway of medium- to long-chain fatty acids no longer than C16, in accordance with the vFAD activity. Our findings suggest that cyanophages are capable of fiddling with the infected host’s membranes, possibly leading to increased photoprotection and potentially enhancing viral-encoded photosynthetic proteins, resulting in a new viral metabolic network.
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19
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Fridman S, Flores-Uribe J, Larom S, Alalouf O, Liran O, Yacoby I, Salama F, Bailleul B, Rappaport F, Ziv T, Sharon I, Cornejo-Castillo FM, Philosof A, Dupont CL, Sánchez P, Acinas SG, Rohwer FL, Lindell D, Béjà O. A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells. Nat Microbiol 2017; 2:1350-1357. [PMID: 28785078 DOI: 10.1038/s41564-017-0002-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 06/28/2017] [Indexed: 01/27/2023]
Abstract
Cyanobacteria are important contributors to primary production in the open oceans. Over the past decade, various photosynthesis-related genes have been found in viruses that infect cyanobacteria (cyanophages). Although photosystem II (PSII) genes are common in both cultured cyanophages and environmental samples 1-4 , viral photosystem I (vPSI) genes have so far only been detected in environmental samples 5,6 . Here, we have used a targeted strategy to isolate a cyanophage from the tropical Pacific Ocean that carries a PSI gene cassette with seven distinct PSI genes (psaJF, C, A, B, K, E, D) as well as two PSII genes (psbA, D). This cyanophage, P-TIM68, belongs to the T4-like myoviruses, has a prolate capsid, a long contractile tail and infects Prochlorococcus sp. strain MIT9515. Phage photosynthesis genes from both photosystems are expressed during infection, and the resultant proteins are incorporated into membranes of the infected host. Moreover, photosynthetic capacity in the cell is maintained throughout the infection cycle with enhancement of cyclic electron flow around PSI. Analysis of metagenomic data from the Tara Oceans expedition 7 shows that phages carrying PSI gene cassettes are abundant in the tropical Pacific Ocean, composing up to 28% of T4-like cyanomyophages. They are also present in the tropical Indian and Atlantic Oceans. P-TIM68 populations, specifically, compose on average 22% of the PSI-gene-cassette carrying phages. Our results suggest that cyanophages carrying PSI and PSII genes are likely to maintain and even manipulate photosynthesis during infection of their Prochlorococcus hosts in the tropical oceans.
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Affiliation(s)
- Svetlana Fridman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - José Flores-Uribe
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Shirley Larom
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Onit Alalouf
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Oded Liran
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Iftach Yacoby
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Faris Salama
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS and Université Pierre et Marie Curie, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabrice Rappaport
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS and Université Pierre et Marie Curie, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Tamar Ziv
- Smoler Proteomics Center, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona, 11016, Israel.,Tel Hai College, Upper Galilee, 12210, Israel
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, 08003, Barcelona, Spain
| | - Alon Philosof
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, 08003, Barcelona, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, 08003, Barcelona, Spain
| | - Forest L Rohwer
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Debbie Lindell
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
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20
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Two Synechococcus genes, Two Different Effects on Cyanophage Infection. Viruses 2017; 9:v9060136. [PMID: 28574452 PMCID: PMC5490813 DOI: 10.3390/v9060136] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 12/12/2022] Open
Abstract
Synechococcus is an abundant marine cyanobacterium that significantly contributes to primary production. Lytic phages are thought to have a major impact on cyanobacterial population dynamics and evolution. Previously, an investigation of the transcriptional response of three Synechococcus strains to infection by the T4-like cyanomyovirus, Syn9, revealed that while the transcript levels of the vast majority of host genes declined soon after infection, those for some genes increased or remained stable. In order to assess the role of two such host-response genes during infection, we inactivated them in Synechococcus sp. strain WH8102. One gene, SYNW1659, encodes a domain of unknown function (DUF3387) that is associated with restriction enzymes. The second gene, SYNW1946, encodes a PIN-PhoH protein, of which the PIN domain is common in bacterial toxin-antitoxin systems. Neither of the inactivation mutations impacted host growth or the length of the Syn9 lytic cycle. However, the DUF3387 mutant supported significantly lower phage DNA replication and yield of phage progeny than the wild-type, suggesting that the product of this host gene aids phage production. The PIN-PhoH mutant, on the other hand, allowed for significantly higher Syn9 genomic DNA replication and progeny production, suggesting that this host gene plays a role in restraining the infection process. Our findings indicate that host-response genes play a functional role during infection and suggest that some function in an attempt at defense against the phage, while others are exploited by the phage for improved infection.
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21
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Genetic hurdles limit the arms race between Prochlorococcus and the T7-like podoviruses infecting them. ISME JOURNAL 2017; 11:1836-1851. [PMID: 28440802 PMCID: PMC5520035 DOI: 10.1038/ismej.2017.47] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 01/31/2017] [Accepted: 02/28/2017] [Indexed: 01/21/2023]
Abstract
Phages and hosts coexist in nature with a high degree of population diversity. This is often explained through coevolutionary models, such as the arms race or density-dependent fluctuating selection, which differ in assumptions regarding the emergence of phage mutants that overcome host resistance. Previously, resistance in the abundant marine cyanobacterium, Prochlorococcus, was found to occur frequently. However, little is known about the ability of phages to overcome this resistance. Here we report that, in some cases, T7-like cyanophage mutants emerge to infect resistant Prochlorococcus strains. These resistance-breaking phages retained the ability to infect the wild-type host. However, fitness of the mutant phages differed on the two hosts. Furthermore, in one case, resistance-breaking was accompanied by costs of decreased fitness on the wild-type host and decreased adsorption specificity, relative to the wild-type phage. In two other cases, fitness on the wild-type host increased. Whole-genome sequencing revealed mutations in probable tail-related genes. These were highly diverse in isolates and natural populations of T7-like cyanophages, suggesting that antagonistic coevolution enhances phage genome diversity. Intriguingly, most interactions did not yield resistance-breaking phages. Thus, resistance mutations raise genetic barriers to continuous arms race cycles and are indicative of an inherent asymmetry in coevolutionary capacity, with hosts having the advantage. Nevertheless, phages coexist with hosts, which we propose relies on combined, parallel action of a limited arms race, fluctuating selection and passive host-switching within diverse communities. Together, these processes generate a constantly changing network of interactions, enabling stable coexistence between hosts and phages in nature.
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22
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Kirzner S, Barak E, Lindell D. Variability in progeny production and virulence of cyanophages determined at the single-cell level. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:605-613. [PMID: 27084786 DOI: 10.1111/1758-2229.12409] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Little information regarding viral progeny production (burst size) and host mortality (viral virulence) is currently available for environmentally relevant phages. This is partially due to the difficulty in accurately measuring these infection properties with existing methods. Here, we set up a simple system for determining viral virulence and burst size at the single-cell level following flow cytometric separation of infected cells. We applied this assay to two distinct cyanomyoviruses, Syn9 and S-TIM5, during infection of two marine Synechococcus strains each. We found that virulence ranged from 44%-82%, differing for the same phage on different hosts. Average burst sizes ranged from 21-43 infective viruses/cell, and differed with host for Syn9, whereas the burst size of S-TIM5 was similar for both hosts. In addition, virulence and burst sizes were different for the two phages when infecting their common host. Furthermore, wide-ranging cell-to-cell variability was found for single-cell burst sizes in each of the four interactions, ranging from 2 to over 100 infective viruses/cell. This variability, discerned at both the population and single-cell levels under controlled laboratory conditions, is likely to be much more complex in natural environments.
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Affiliation(s)
- Shay Kirzner
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Efrat Barak
- Life Sciences and Engineering Infrastructure Unit, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Debbie Lindell
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
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Domínguez-Martín MA, Díez J, García-Fernández JM. Physiological Studies of Glutamine Synthetases I and III from Synechococcus sp. WH7803 Reveal Differential Regulation. Front Microbiol 2016; 7:969. [PMID: 27446010 PMCID: PMC4923085 DOI: 10.3389/fmicb.2016.00969] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/03/2016] [Indexed: 11/18/2022] Open
Abstract
The marine picocyanobacterium Synechococcus sp. WH7803 possesses two glutamine synthetases (GSs; EC 6.3.1.2), GSI encoded by glnA and GSIII encoded by glnN. This is the first work addressing the physiological regulation of both enzymes in a marine cyanobacterial strain. The increase of GS activity upon nitrogen starvation was similar to that found in other model cyanobacteria. However, an unusual response was found when cells were grown under darkness: the GS activity was unaffected, reflecting adaptation to the environment where they thrive. On the other hand, we found that GSIII did not respond to nitrogen availability, in sharp contrast with the results observed for this enzyme in other cyanobacteria thus far studied. These features suggest that GS activities in Synechococcus sp. WH7803 represent an intermediate step in the evolution of cyanobacteria, in a process of regulatory streamlining where GSI lost the regulation by light, while GSIII lost its responsiveness to nitrogen. This is in good agreement with the phylogeny of Synechococcus sp. WH7803 in the context of the marine cyanobacterial radiation.
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Affiliation(s)
| | | | - José M. García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de CórdobaCórdoba, Spain
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Transcriptome dynamics of a broad host-range cyanophage and its hosts. ISME JOURNAL 2015; 10:1437-55. [PMID: 26623542 DOI: 10.1038/ismej.2015.210] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/17/2015] [Accepted: 10/07/2015] [Indexed: 01/21/2023]
Abstract
Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host-ranges relative to other cyanophages. It is currently unknown whether broad host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. Here we used microarray and RNA-seq analyses to investigate the interaction between the Syn9 T4-like cyanophage and three phylogenetically, ecologically and genomically distinct marine Synechococcus strains: WH7803, WH8102 and WH8109. Strikingly, Syn9 led a nearly identical infection and transcriptional program in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporally regulated gene expression classes were observed. Furthermore, a novel regulatory element controlled early-gene transcription, and host-like promoters drove middle gene transcription, different to the regulatory paradigm for T4. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A. Moreover, genomic and metagenomic analyses indicate that these regulatory elements are abundant and conserved among T4-like cyanophages. In contrast to the near-identical transcriptional program employed by Syn9, host responses to infection involved host-specific genes primarily located in hypervariable genomic islands, substantiating islands as a major axis of phage-cyanobacteria interactions. Our findings suggest that the ability of broad host-range phages to infect multiple hosts is more likely dependent on the effectiveness of host defense strategies than on differential tailoring of the infection process by the phage.
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Saito MA, McIlvin MR, Moran DM, Goepfert TJ, DiTullio GR, Post AF, Lamborg CH. Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers. Science 2014; 345:1173-7. [PMID: 25190794 DOI: 10.1126/science.1256450] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Marine primary productivity is strongly influenced by the scarcity of required nutrients, yet our understanding of these nutrient limitations is informed by experimental observations with sparse geographical coverage and methodological limitations. We developed a quantitative proteomic method to directly assess nutrient stress in high-light ecotypes of the abundant cyanobacterium Prochlorococcus across a meridional transect in the central Pacific Ocean. Multiple peptide biomarkers detected widespread and overlapping regions of nutritional stress for nitrogen and phosphorus in the North Pacific Subtropical Gyre and iron in the equatorial Pacific. Quantitative protein analyses demonstrated simultaneous stress for these nutrients at biome interfaces. This application of proteomic biomarkers to diagnose ocean metabolism demonstrated Prochlorococcus actively and simultaneously deploying multiple biochemical strategies for low-nutrient conditions in the oceans.
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Affiliation(s)
- Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
| | - Matthew R McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Dawn M Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Tyler J Goepfert
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | | | - Anton F Post
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Carl H Lamborg
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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26
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Dekel-Bird NP, Sabehi G, Mosevitzky B, Lindell D. Host-dependent differences in abundance, composition and host range of cyanophages from the Red Sea. Environ Microbiol 2014; 17:1286-99. [DOI: 10.1111/1462-2920.12569] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 07/15/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Naama P. Dekel-Bird
- Faculty of Biology; Technion - Israel Institute of Technology; Haifa 32000 Israel
| | - Gazalah Sabehi
- Faculty of Biology; Technion - Israel Institute of Technology; Haifa 32000 Israel
| | - Bar Mosevitzky
- Faculty of Biology; Technion - Israel Institute of Technology; Haifa 32000 Israel
| | - Debbie Lindell
- Faculty of Biology; Technion - Israel Institute of Technology; Haifa 32000 Israel
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Vareli K, Jaeger W, Touka A, Frillingos S, Briasoulis E, Sainis I. Hepatotoxic seafood poisoning (HSP) due to microcystins: a threat from the ocean? Mar Drugs 2013; 11:2751-68. [PMID: 23921721 PMCID: PMC3766863 DOI: 10.3390/md11082751] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/15/2013] [Accepted: 07/16/2013] [Indexed: 01/11/2023] Open
Abstract
Cyanobacterial blooms are a major and growing problem for freshwater ecosystems worldwide that increasingly concerns public health, with an average of 60% of blooms known to be toxic. The most studied cyanobacterial toxins belong to a family of cyclic heptapeptide hepatotoxins, called microcystins. The microcystins are stable hydrophilic cyclic heptapeptides with a potential to cause cell damage following cellular uptake via organic anion-transporting proteins (OATP). Their intracellular biologic effects presumably involve inhibition of catalytic subunits of protein phosphatases (PP1 and PP2A) and glutathione depletion. The microcystins produced by cyanobacteria pose a serious problem to human health, if they contaminate drinking water or food. These toxins are collectively responsible for human fatalities, as well as continued and widespread poisoning of wild and domestic animals. Although intoxications of aquatic organisms by microcystins have been widely documented for freshwater ecosystems, such poisonings in marine environments have only occasionally been reported. Moreover, these poisonings have been attributed to freshwater cyanobacterial species invading seas of lower salinity (e.g., the Baltic) or to the discharge of freshwater microcystins into the ocean. However, recent data suggest that microcystins are also being produced in the oceans by a number of cosmopolitan marine species, so that Hepatotoxic Seafood Poisoning (HSP) is increasingly recognized as a major health risk that follows consumption of contaminated seafood.
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Affiliation(s)
- Katerina Vareli
- Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece; E-Mail:
- Interscience Molecular Oncology Laboratory, Human Cancer Biobank Center, University of Ioannina, 45110 Ioannina, Greece; E-Mails: (A.T.); (E.B.)
| | - Walter Jaeger
- Department of Clinical Pharmacy and Diagnostics, University of Vienna, A-1090 Vienna, Austria; E-Mail:
| | - Anastasia Touka
- Interscience Molecular Oncology Laboratory, Human Cancer Biobank Center, University of Ioannina, 45110 Ioannina, Greece; E-Mails: (A.T.); (E.B.)
| | - Stathis Frillingos
- Laboratory of Biological Chemistry, School of Medicine, University of Ioannina, 45110 Ioannina, Greece; E-Mail:
| | - Evangelos Briasoulis
- Interscience Molecular Oncology Laboratory, Human Cancer Biobank Center, University of Ioannina, 45110 Ioannina, Greece; E-Mails: (A.T.); (E.B.)
| | - Ioannis Sainis
- Interscience Molecular Oncology Laboratory, Human Cancer Biobank Center, University of Ioannina, 45110 Ioannina, Greece; E-Mails: (A.T.); (E.B.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +30-26-510-075-57; Fax: +30-26-510-070-64
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Post AF, Rihtman B, Wang Q. Decoupling of ammonium regulation and ntcA transcription in the diazotrophic marine cyanobacterium Trichodesmium sp. IMS101. THE ISME JOURNAL 2012; 6:629-37. [PMID: 21938021 PMCID: PMC3280139 DOI: 10.1038/ismej.2011.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/03/2011] [Accepted: 08/03/2011] [Indexed: 11/09/2022]
Abstract
Nitrogen (N) physiology in the marine cyanobacterium Trichodesmium IMS101 was studied along with transcript accumulation of the N-regulatory gene ntcA and of two of its target genes: napA (nitrate assimilation) and nifH (N(2) fixation). N(2) fixation was impaired in the presence of nitrite, nitrate and urea. Strain IMS101 was capable of growth on these combined N sources at <2 μM but growth rates declined at elevated concentrations. Assimilation of nitrate and urea was impaired in the presence of ammonium. Whereas ecologically relevant N concentrations (2-20 μM) suppressed growth and assimilation, much higher concentrations were required to affect transcript levels. Transcripts of nifH accumulated under nitrogen-fixing conditions; these transcript levels were maintained in the presence of nitrate (100 μM) and ammonium (20 μM). However, nifH transcript levels were below detection at ammonium concentrations >20 μM. napA mRNA was found at low levels in both N(2)-fixing and ammonium-utilizing filaments, and it accumulated in filaments grown with nitrate. The positive effect of nitrate on napA transcription was abolished by ammonium additions of >200 μM. This effect was restored upon addition of the glutamine synthetase inhibitor L-methionin-DL-sulfoximine. Surprisingly, ntcA transcript levels remained high in the presence of ammonium, even at elevated concentrations. These findings indicate that ammonium repression is decoupled from transcriptional activation of ntcA in Trichodesmium IMS101.
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Affiliation(s)
- Anton F Post
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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Mazard S, Wilson WH, Scanlan DJ. DISSECTING THE PHYSIOLOGICAL RESPONSE TO PHOSPHORUS STRESS IN MARINE SYNECHOCOCCUS ISOLATES (CYANOPHYCEAE)(1). JOURNAL OF PHYCOLOGY 2012; 48:94-105. [PMID: 27009654 DOI: 10.1111/j.1529-8817.2011.01089.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Marine Synechococcus is ubiquitous in aquatic environments. However, distinct phylogenetic lineages of this genus have a complex ecological distribution that is not fully explained. Here, we undertook a broad study of the phosphorus (P)-related behavior of marine Synechococcus isolates from all previously described ribotypes (sensu Fuller et al. 2003). A wide variability in P-related physiology was noted among members of this genus, particularly in the utilization of organic P sources. However, some characteristics (e.g., cell size change during P limitation and the ability to accumulate polyphosphate) were largely consistent with their phylogenetic lineage and inferred ecology, with clear distinctions between oligotrophic, mesotrophic, and opportunistic lineages. Similarly, the ability to induce protein expression in response to P limitation was consistent with the presence/absence of phoB/R regulatory capacity of the corresponding strain. Taxonomic differences in P uptake, storage, and utilization strategies could explain the ubiquitous distribution of marine Synechococcus throughout the world's oceans and explain the coexistence and/or ecological partitioning of multiple phototrophic taxa in the photic zone of tropical and subtropical oligotrophic oceans.
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Affiliation(s)
- Sophie Mazard
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK Plymouth Marine Laboratory, Plymouth, PL1 3DH, UK Bigelow Laboratory for Ocean Sciences, Maine 04575, USASchool of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - William H Wilson
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK Plymouth Marine Laboratory, Plymouth, PL1 3DH, UK Bigelow Laboratory for Ocean Sciences, Maine 04575, USASchool of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Dave J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK Plymouth Marine Laboratory, Plymouth, PL1 3DH, UK Bigelow Laboratory for Ocean Sciences, Maine 04575, USASchool of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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Collier JL, Lovindeer R, Xi Y, Radway JC, Armstrong RA. DIFFERENCES IN GROWTH AND PHYSIOLOGY OF MARINE SYNECHOCOCCUS (CYANOBACTERIA) ON NITRATE VERSUS AMMONIUM ARE NOT DETERMINED SOLELY BY NITROGEN SOURCE REDOX STATE(1). JOURNAL OF PHYCOLOGY 2012; 48:106-116. [PMID: 27009655 DOI: 10.1111/j.1529-8817.2011.01100.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The preference of phytoplankton for ammonium over nitrate has traditionally been explained by the greater metabolic cost of reducing oxidized forms of nitrogen. This "metabolic cost hypothesis" implies that there should be a growth disadvantage on nitrate compared to ammonium or other forms of reduced nitrogen such as urea, especially when light limits growth, but in a variety of phytoplankton taxa, this predicted difference has not been observed. Our experiments with three strains of marine Synechococcus (WH7803, WH7805, and WH8112) did not reveal consistently faster growth (cell division) on ammonium or urea as compared to nitrate. Urease and glutamine synthetase (GS) activities varied with nitrogen source in a manner consistent with regulation by cellular nitrogen status via NtcA (rather than by external availability of nitrogen) in all three strains and indicated that each strain experienced some degree of nitrogen insufficiency during growth on nitrate. At light intensities that strongly limited growth, the composition (carbon, nitrogen, and pigment quotas) of WH7805 cells using nitrate was indistinguishable from that of cells using ammonium, but at saturating light intensities, cellular carbon, nitrogen, and pigment quotas were significantly lower in cells using nitrate than ammonium. These and similar results from other phytoplankton taxa suggest that a limitation in some step of nitrate uptake or assimilation, rather than the extra cost of reducing nitrate per se, may be the cause of differences in growth and physiology between cells using nitrate and ammonium.
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Affiliation(s)
- Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USABiology Department, Rensselaer Polytechnic Institute, Troy, New York 12180, USASchool of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USA
| | - Raisha Lovindeer
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USABiology Department, Rensselaer Polytechnic Institute, Troy, New York 12180, USASchool of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USA
| | - Yue Xi
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USABiology Department, Rensselaer Polytechnic Institute, Troy, New York 12180, USASchool of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USA
| | - JoAnn C Radway
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USABiology Department, Rensselaer Polytechnic Institute, Troy, New York 12180, USASchool of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USA
| | - Robert A Armstrong
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USABiology Department, Rensselaer Polytechnic Institute, Troy, New York 12180, USASchool of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USA
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Post AF, Penno S, Zandbank K, Paytan A, Huse SM, Welch DM. Long term seasonal dynamics of synechococcus population structure in the gulf of aqaba, northern red sea. Front Microbiol 2011; 2:131. [PMID: 21734910 PMCID: PMC3122069 DOI: 10.3389/fmicb.2011.00131] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 05/27/2011] [Indexed: 11/13/2022] Open
Abstract
Spatial patterns of marine Synechococcus diversity across ocean domains have been reported on extensively. However, much less is known of seasonal and multiannual patterns of change in Synechococcus community composition. Here we report on the genotypic diversity of Synechococcus populations in the Gulf of Aqaba, Northern Red Sea, over seven annual cycles of deep mixing and stabile stratification, using ntcA as a phylogenetic marker. Synechococcus clone libraries were dominated by clade II and XII genotypes and a total of eight different clades were identified. Inclusion of ntcA sequences from the Global Ocean Sampling database in our analyses identified members of clade XII from beyond the Gulf of Aqaba, extending its known distribution. Most of the Synechococcus diversity was attributed to members of clade II during the spring bloom, while clade III contributed significantly to diversity during summer stratification. Clade XII diversity was most prevalent in fall and winter. Clade abundances were estimated from pyrosequencing of the V6 hypervariable region of 16S rRNA. Members of clade II dominated Synechococcus communities throughout the year, whereas the less frequent genotypes showed a pattern of seasonal succession. Based on the prevailing nutritional conditions we observed that clade I members thrive at higher nutrient concentrations during winter mixing. Clades V, VI and X became apparent during the transition periods between mixing and stratification. Clade III became prominent during sumeer stratification. We propose that members of clades V, VI, and X, and clade III are Synechococcus ecotypes that are adapted to intermediate and low nutrient levels respectively. This is the first time that molecular analyses have correlated population dynamics of Synechococcus genotypes with temporal fluctuations in nutrient regimes. Since these Synechococcus genotypes are routinely observed in the Gulf of Aqaba we suggest that seasonal fluctuations in nutrient levels create temporal niches that sustain their coexistence.
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Affiliation(s)
- Anton F Post
- Marine Biological Laboratory, The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole, MA, USA
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Intracellular assembly of cyanophage Syn5 proceeds through a scaffold-containing procapsid. J Virol 2010; 85:2406-15. [PMID: 21177804 DOI: 10.1128/jvi.01601-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Syn5 is a marine cyanophage that is propagated on the marine photosynthetic cyanobacterial strain Synechococcus sp. WH8109 under laboratory conditions. Cryoelectron images of this double-stranded DNA (dsDNA) phage reveal an icosahedral capsid with short tail appendages and a single novel hornlike structure at the vertex opposite the tail. Despite the major impact of cyanophages on life in the oceans, there is limited information on cyanophage intracellular assembly processes within their photosynthetic hosts. The one-step growth curve of Syn5 demonstrated a short cycle with an eclipse period of ∼45 min, a latent phase of ∼60 min, and a burst size of 20 to 30 particles per cell at 28°C. SDS-PAGE and Western blot analysis of cell lysates at different times after infection showed the synthesis of major virion proteins and their increase as the infection progressed. The scaffolding protein of Syn5, absent from virions, was identified in the lysates and expressed from the cloned gene. It migrated anomalously on SDS-PAGE, similar to the phage T7 scaffolding protein. Particles lacking DNA but containing the coat and scaffolding proteins were purified from Syn5-infected cells using CsCl centrifugation followed by sucrose gradient centrifugation. Electron microscopic images of the purified particles showed shells lacking condensed DNA but filled with protein density, presumably scaffolding protein. These findings suggest that the cyanophages form infectious virions through the initial assembly of scaffolding-containing procapsids, similar to the assembly pathways for the enteric dsDNA bacteriophages. Since cyanobacteria predate the enteric bacteria, this procapsid-mediated assembly pathway may have originated with the cyanophages.
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NtcA from Microcystis aeruginosa PCC 7806 is autoregulatory and binds to the microcystin promoter. Appl Environ Microbiol 2010; 76:4362-8. [PMID: 20453121 DOI: 10.1128/aem.01862-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NtcA is a transcription factor that has been found in a diverse range of cyanobacteria. This nitrogen-controlled factor was focused on as a key component in the yet-to-be-deciphered regulatory network controlling microcystin production. Adaptor-mediated PCR was utilized to isolate the ntcA gene from Microcystis aeruginosa PCC 7806. This gene was cloned, and the recombinant (His-tagged) protein was overexpressed and purified for use in mobility shift assays to analyze NtcA binding to putative sites identified in the microcystin mcyA/D promoter region. Autoregulation of NtcA in M. aeruginosa was shown via NtcA binding in the upstream ntcA promoter region. The observation of binding of NtcA to the mcyA/D promoter region has direct relevance for the regulation of microcystin biosynthesis, as transcription of the mcyABCDEFGHIJ gene cluster appears to be under direct control of nitrogen.
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Ostrowski M, Mazard S, Tetu SG, Phillippy K, Johnson A, Palenik B, Paulsen IT, Scanlan DJ. PtrA is required for coordinate regulation of gene expression during phosphate stress in a marine Synechococcus. ISME JOURNAL 2010; 4:908-21. [PMID: 20376102 DOI: 10.1038/ismej.2010.24] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Previous microarray analyses have shown a key role for the two-component system PhoBR (SYNW0947, SYNW0948) in the regulation of P transport and metabolism in the marine cyanobacterium Synechococcus sp. WH8102. However, there is some evidence that another regulator, SYNW1019 (PtrA), probably under the control of PhoBR, is involved in the response to P depletion. PtrA is a member of the cAMP receptor protein transcriptional regulator family that shows homology to NtcA, the global nitrogen regulator in cyanobacteria. To define the role of this regulator, we constructed a mutant by insertional inactivation and compared the physiology of wild-type Synechcococcus sp. WH8102 with the ptrA mutant under P-replete and P-stress conditions. In response to P stress the ptrA mutant failed to upregulate phosphatase activity. Microarrays and quantitative RT-PCR indicate that a subset of the Pho regulon is controlled by PtrA, including two phosphatases, a predicted phytase and a gene of unknown function psip1 (SYNW0165), all of which are highly upregulated during P limitation. Electrophoretic mobility shift assays indicate binding of overexpressed PtrA to promoter sequences upstream of the induced genes. This work suggests a two-tiered response to P depletion in this strain, the first being PhoB-dependent induction of high-affinity PO(4) transporters, and the second the PtrA-dependent induction of phosphatases for scavenging organic P. The levels of numerous other transcripts are also directly or indirectly influenced by PtrA, including those involved in cell-surface modification, metal uptake, photosynthesis, stress responses and other metabolic processes, which may indicate a wider role for PtrA in cellular regulation in marine picocyanobacteria.
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Affiliation(s)
- Martin Ostrowski
- Department of Biological Sciences, University of Warwick, Coventry, UK
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Jones AC, Gerwick L, Gonzalez D, Dorrestein PC, Gerwick WH. Transcriptional analysis of the jamaicamide gene cluster from the marine cyanobacterium Lyngbya majuscula and identification of possible regulatory proteins. BMC Microbiol 2009; 9:247. [PMID: 19951434 PMCID: PMC2799420 DOI: 10.1186/1471-2180-9-247] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Accepted: 12/01/2009] [Indexed: 12/02/2022] Open
Abstract
Background The marine cyanobacterium Lyngbya majuscula is a prolific producer of bioactive secondary metabolites. Although biosynthetic gene clusters encoding several of these compounds have been identified, little is known about how these clusters of genes are transcribed or regulated, and techniques targeting genetic manipulation in Lyngbya strains have not yet been developed. We conducted transcriptional analyses of the jamaicamide gene cluster from a Jamaican strain of Lyngbya majuscula, and isolated proteins that could be involved in jamaicamide regulation. Results An unusually long untranslated leader region of approximately 840 bp is located between the jamaicamide transcription start site (TSS) and gene cluster start codon. All of the intergenic regions between the pathway ORFs were transcribed into RNA in RT-PCR experiments; however, a promoter prediction program indicated the possible presence of promoters in multiple intergenic regions. Because the functionality of these promoters could not be verified in vivo, we used a reporter gene assay in E. coli to show that several of these intergenic regions, as well as the primary promoter preceding the TSS, are capable of driving β-galactosidase production. A protein pulldown assay was also used to isolate proteins that may regulate the jamaicamide pathway. Pulldown experiments using the intergenic region upstream of jamA as a DNA probe isolated two proteins that were identified by LC-MS/MS. By BLAST analysis, one of these had close sequence identity to a regulatory protein in another cyanobacterial species. Protein comparisons suggest a possible correlation between secondary metabolism regulation and light dependent complementary chromatic adaptation. Electromobility shift assays were used to evaluate binding of the recombinant proteins to the jamaicamide promoter region. Conclusion Insights into natural product regulation in cyanobacteria are of significant value to drug discovery and biotechnology. To our knowledge, this is the first attempt to characterize the transcription and regulation of secondary metabolism in a marine cyanobacterium. If jamaicamide is light regulated, this mechanism would be similar to other cyanobacterial natural product gene clusters such as microcystin LR. These findings could aid in understanding and potentially assisting the management of toxin production by Lyngbya in the environment.
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Affiliation(s)
- Adam C Jones
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Use of inorganic and organic nitrogen by Synechococcus spp. and diatoms on the west Florida shelf as measured using stable isotope probing. Appl Environ Microbiol 2009; 75:6662-70. [PMID: 19734334 DOI: 10.1128/aem.01002-09] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine nitrogen (N) cycle is a complex network of biological transformations in different N pools. The linkages among these different reservoirs are often poorly understood. Traditional methods for measuring N uptake rely on bulk community properties and cannot provide taxonomic information. (15)N-based stable isotope probing (SIP), however, is a technique that allows detection of uptake of individual N sources by specific microorganisms. In this study we used (15)N SIP methodology to assess the use of different nitrogen substrates by Synechococcus spp. and diatoms on the west Florida shelf. Seawater was incubated in the presence of (15)N-labeled ammonium, nitrate, urea, glutamic acid, and a mixture of 16 amino acids. DNA was extracted and fractionated using CsCl density gradient centrifugation. Quantitative PCR was used to quantify the amounts of Synechococcus and diatom DNA as a function of density, and (15)N tracer techniques were used to measure rates of N uptake by the microbial community. The ammonium, nitrate, urea, and dissolved primary amine uptake rates were 0.077, 0.065, 0.013, and 0.055 micromol N liter(-1) h(-1), respectively. SIP data indicated that diatoms and Synechococcus spp. actively incorporated N from [(15)N]nitrate, [(15)N]ammonium, and [(15)N]urea. Synechococcus also incorporated nitrogen from [(15)N]glutamate and (15)N-amino acids, but no evidence indicating uptake of labeled amino acids by diatoms was detected. These data suggest that N flow in communities containing Synechococcus spp. and diatoms has more plasticity than the new-versus-recycled production paradigm suggests and that these phytoplankters should not be viewed strictly as recycled and new producers, respectively.
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Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, Post AF, Hagemann M, Paulsen I, Partensky F. Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 2009; 73:249-99. [PMID: 19487728 PMCID: PMC2698417 DOI: 10.1128/mmbr.00035-08] [Citation(s) in RCA: 446] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45 degrees N to 40 degrees S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.
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Affiliation(s)
- D J Scanlan
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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Wyman M, Bird C. Lack of control of nitrite assimilation by ammonium in an oceanic picocyanobacterium, Synechococcus sp. strain WH 8103. Appl Environ Microbiol 2007; 73:3028-33. [PMID: 17337543 PMCID: PMC1892888 DOI: 10.1128/aem.02606-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In cyanobacteria, the transcriptional activator NtcA is involved in global nitrogen control and, in the absence of ammonium, regulates the expression of genes involved in the assimilation of alternative nitrogen sources. The oceanic picocyanobacterium Synechococcus sp. strain WH 8103 harbors a copy of ntcA, but in the present study, we show that unlike other marine cyanobacteria that have been investigated, this strain is capable of coassimilating nitrite when grown in the presence of ammonium. Transcript levels for the genes encoding the nitrate/nitrite-bispecific permease NrtP and nitrate reductase (NarB) were substantially down-regulated by ammonium, whereas the abundances of nitrite reductase (NirA) transcripts were similar in nitrite- and ammonium-grown cells. The growth of Synechococcus sp. strain WH 8103 in medium containing both ammonium and nitrite resulted in only minor changes in the expression profile in comparison to that of nitrite-grown cells with the exception that the gene encoding the high-affinity ammonium transporter Amt1 was down-regulated to the levels seen in ammonium-grown cells. Whereas the expression of nrtP, narB, and amt1 appears to be NtcA dependent in this marine cyanobacterium, the transcription and expression of nirA appear not to be. The ability to coassimilate nitrite and reduced-nitrogen sources like ammonium may be an adaptive trait that enables oceanic strains like Synechococcus sp. strain WH 8103 to exploit the low nitrite concentrations found in oceanic surface waters that are not available to their principal and more numerous competitor, Prochlorococcus.
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Affiliation(s)
- Michael Wyman
- School of Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom.
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Penno S, Lindell D, Post AF. Diversity of Synechococcus and Prochlorococcus populations determined from DNA sequences of the N-regulatory gene ntcA. Environ Microbiol 2006; 8:1200-11. [PMID: 16817928 DOI: 10.1111/j.1462-2920.2006.01010.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cyanobacteria Synechococcus and Prochlorococcus are abundant primary producers in the nitrogen-poor waters of the Gulf of Aqaba, northern Red Sea. Expression of the nitrogen regulatory gene ntcA is a useful indicator for determining the N-status of cyanobacteria, and preliminary work with this gene suggests that it may also serve as a useful biodiversity marker. Here we investigated the genotypic diversity of ntcA among the full spectrum of cultured Synechococcus and Prochlorococcus lineages and assessed cyanobacterial genotypic composition in environmental samples from the Gulf of Aqaba. The high level of ntcA diversification established this gene as an excellent biodiversity marker capable of distinguishing between numerous clades within each genus with high resolution. An unexpected large diversity was observed among Synechococcus populations, including the detection of four novel clades for which culture representatives have yet to be isolated. In addition, extensive microdiversity within a number of Synechococcus clades was revealed. Temporal differences in the detection of the various Synechococcus clades suggest seasonal fluctuations in the genotypic make-up of Synechococcus populations. In contrast, virtually all Prochlorococcus sequences fell within a single high-light adapted clade that was detected year round. We suggest that the limited genotypic diversity among Prochlorococcus in combination with a limited capacity for acclimation to environmental changes resulting from its small genome size led to the dramatic rise and demise of Prochlorococcus populations over the yearly cycle in the Gulf of Aqaba.
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Affiliation(s)
- Sigrid Penno
- H. Steinitz Marine Biology Laboratory, Interuniversity Institute for Marine Sciences, PO Box 469, Eilat 88103, Israel
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García-Fernández JM, de Marsac NT, Diez J. Streamlined regulation and gene loss as adaptive mechanisms in Prochlorococcus for optimized nitrogen utilization in oligotrophic environments. Microbiol Mol Biol Rev 2005; 68:630-8. [PMID: 15590777 PMCID: PMC539009 DOI: 10.1128/mmbr.68.4.630-638.2004] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Prochlorococcus is one of the dominant cyanobacteria and a key primary producer in oligotrophic intertropical oceans. Here we present an overview of the pathways of nitrogen assimilation in Prochlorococcus, which have been significantly modified in these microorganisms for adaptation to the natural limitations of their habitats, leading to the appearance of different ecotypes lacking key enzymes, such as nitrate reductase, nitrite reductase, or urease, and to the simplification of the metabolic regulation systems. The only nitrogen source utilizable by all studied isolates is ammonia, which is incorporated into glutamate by glutamine synthetase. However, this enzyme shows unusual regulatory features, although its structural and kinetic features are unchanged. Similarly, urease activities remain fairly constant under different conditions. The signal transduction protein P(II) is apparently not phosphorylated in Prochlorococcus, despite its conserved amino acid sequence. The genes amt1 and ntcA (coding for an ammonium transporter and a global nitrogen regulator, respectively) show noncorrelated expression in Prochlorococcus under nitrogen stress; furthermore, high rates of organic nitrogen uptake have been observed. All of these unusual features could provide a physiological basis for the predominance of Prochlorococcus over Synechococcus in oligotrophic oceans.
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Affiliation(s)
- Jose Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, Planta 1, Campus de Rabanales, 14071-Córdoba, Spain.
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Valladares A, Muro-Pastor AM, Herrero A, Flores E. The NtcA-dependent P1 promoter is utilized for glnA expression in N2-fixing heterocysts of Anabaena sp. strain PCC 7120. J Bacteriol 2004; 186:7337-43. [PMID: 15489445 PMCID: PMC523192 DOI: 10.1128/jb.186.21.7337-7343.2004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of the glnA gene encoding glutamine synthetase, a key enzyme in nitrogen metabolism, is subject to a variety of regulatory mechanisms in different organisms. In the filamentous, N(2)-fixing cyanobacterium Anabaena sp. strain PCC 7120, glnA is expressed from multiple promoters that generate several transcripts whose abundance is influenced by NtcA, the transcription factor exerting global nitrogen control in cyanobacteria. Whereas RNA(I) originates from a canonical NtcA-dependent promoter (P(1)) and RNA(II) originates from a sigma(70)-type promoter (P(2)), RNA(IV) is influenced by NtcA but the corresponding promoter (P(3)) does not have the structure of NtcA-activated promoters. Using RNA isolated from Anabaena filaments grown under different nitrogen regimens, we observed, in addition to these transcripts, RNA(V), which has previously been detected only in in vitro transcription assays and should originate from P(4). However, in heterocysts, which are differentiated cells specialized in N(2) fixation, RNA(I) was the almost exclusive glnA transcript. Analysis of P(glnA)::lacZ fusions containing different fragments of the glnA upstream region confirmed that fragments carrying P(1), P(2), or P(3) and P(4) have the ability to promote transcription. Mutation of the NtcA-binding site in P(1) eliminated P(1)-directed transcription and allowed increased use of P(2). The NtcA-binding site in the P(1) promoter and binding of NtcA to this site appear to be key factors in determining glnA gene expression in vegetative cells and heterocysts.
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Affiliation(s)
- Ana Valladares
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, Avda. Américo Vespucio s/n, E-41092 Seville, Spain
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Wisén S, Bergman B, Mannervik B. Mutagenesis of the cysteine residues in the transcription factor NtcA from Anabaena PCC 7120 and its effects on DNA binding in vitro. ACTA ACUST UNITED AC 2004; 1679:156-63. [PMID: 15297148 DOI: 10.1016/j.bbaexp.2004.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Revised: 06/08/2004] [Accepted: 06/11/2004] [Indexed: 11/19/2022]
Abstract
NtcA is a transcription factor found in a wide variety of cyanobacteria. It is a key component in the control of the nitrogen metabolism, and regulates genes involved in ammonia assimilation, heterocyst differentiation and nitrogen fixation. NtcA expression is subject to nitrogen control, but there is also evidence that the binding of NtcA to DNA can be regulated by a redox mechanism involving the two cysteine residues in the NtcA protein from Anabaena PCC 7120. In order to investigate this further, the two cysteine residues in NtcA were mutated into alanine to give four variants of the protein: wild-type NtcA, the point-mutated variants Cys157Ala and Cys164Ala, as well as the double mutant Cys157Ala/Cys164Ala. The binding of a DNA probe containing a palindromic NtcA-binding motif was investigated by gel mobility shift analysis under non-reducing and reducing conditions. The experiments show that the DNA binding in vitro is stronger in the presence of the reducing agent DTT than in its absence. However, this effect is not due to breaking of a disulfide bond between the cysteine residues, since the double mutant containing no cysteines was also affected by DTT. A molecular model of a monomer of NtcA, based on the homologous cAMP receptor protein structure, was created in order to locate the positions of the cysteine residues. The NtcA model suggested that the positions of the sulfur atoms are not compatible with formation of a bond between them.
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Affiliation(s)
- Susanne Wisén
- Department of Biochemistry, Uppsala University, Biomedical Center, Box 576, SE-751 23 Uppsala, Sweden
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Bird C, Wyman M. Nitrate/nitrite assimilation system of the marine picoplanktonic cyanobacterium Synechococcus sp. strain WH 8103: effect of nitrogen source and availability on gene expression. Appl Environ Microbiol 2004; 69:7009-18. [PMID: 14660343 PMCID: PMC310010 DOI: 10.1128/aem.69.12.7009-7018.2003] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genes encoding the structural components of the nitrate/nitrite assimilation system of the oceanic cyanobacterium Synechococcus sp. strain WH 8103 were cloned and characterized. The genes encoding nitrate reductase (narB) and nitrite reductase (nirA) are clustered on the chromosome but are organized in separate transcriptional units. Upstream of narB is a homologue of nrtP that encodes a nitrate/nitrite-bispecific permease rather than the components of an ABC-type nitrate transporter found in freshwater cyanobacteria. Unusually, neither nirA nor ntcA (encoding a positive transcription factor of genes subject to nitrogen control) were found to be tightly regulated by ammonium. Furthermore, transcription of glnA (encoding glutamine synthetase) is up-regulated in ammonium-grown cells, highlighting significant differences in nitrogen control in this cyanobacterium. Nitrogen depletion led to the transient up-regulation of ntcA, nirA, nrtP, narB, and glnA in what appears to be an NtcA-dependent manner. The NtcA-like promoters found upstream of nirA, nrtP, and narB all differ in sequence from the canonical NtcA promoter established for other cyanobacteria, and in the case of nirA, the NtcA-like promoter was functional only in cells deprived of combined nitrogen. The ecological implications of these findings are discussed in the context of the oligotrophic nature of oceanic surface waters in which Synechococcus spp. thrive.
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Affiliation(s)
- Clare Bird
- School of Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
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Wang CM, Ekman M, Bergman B. Expression of cyanobacterial genes involved in heterocyst differentiation and dinitrogen fixation along a plant symbiosis development profile. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2004; 17:436-443. [PMID: 15077676 DOI: 10.1094/mpmi.2004.17.4.436] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Members of the cyanobiont genus Nostoc, forming an endosymbiosis with members of the angiosperm genus Gunnera, undergo a number of characteristic phenotypic changes during the development of the symbiosis, the genetic background of which is largely unknown. Transcription patterns of genes related to heterocyst differentiation and dinitrogen fixation and corresponding protein profiles were examined, using reverse transcription-polymerase chain reaction and Western blots, along a developmental (apex to mature parts) sequence in Gunnera magellanica and G. manicata and under mimicked symbiotic conditions in a free-living Gunnera isolate (Nostoc strain 0102). The hetR gene was highly expressed and correlated positively with an increase in heterocyst frequency and with ntcA expression, whereas nifH expression was already high close to the growing apex and glnB (P(II)) expression decreased along the symbiotic profile. Although gene expression appeared to be regulated to a large extent in the same fashion as in free-living cyanobacteria, significant differences were apparent, such as the overexpression of both hetR and ntcA and the contrasting down-regulation of glnB, features indicating important regulatory differences between symbiotic and free-living cyanobacteria. The significance of these findings is discussed in a symbiotic context.
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Affiliation(s)
- Chun-Mei Wang
- Department of Biological Pharmaceutics, School of Chinese Pharmacy, Beijing University of Chinese Medicine, 100029 Beijing, China
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Vogel J, Axmann IM, Herzel H, Hess WR. Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4. Nucleic Acids Res 2003; 31:2890-9. [PMID: 12771216 PMCID: PMC156731 DOI: 10.1093/nar/gkg398] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In contrast to certain model eubacteria, little is known as to where transcription is initiated in the genomes of cyanobacteria, which are largely distinct from other prokaryotes. In this work, 25 transcription start sites (TSS) of 21 different genes of Prochlorococcus sp. MED4 were determined experimentally. The data suggest more than one TSS for the genes ftsZ, petH, psbD and ntcA. In contrast, the rbcL-rbcS operon encoding ribulose 1,5-bisphosphate carboxylase/oxygenase lacks a detectable promoter and is co-transcribed with the upstream located gene ccmK. The entire set of experimental data was used in a genome-wide scan for putative TSS in Prochlorococcus. A -10 element could be defined, whereas at the -35 position there was no element common to all investigated sequences. However, splitting the data set into sub-classes revealed different types of putative -35 boxes. Only one of them resembled the consensus sequence TTGACA recognized by the vegetative sigma factor (sigma70) of enterobacteria. Using a scoring matrix of the -10 element, more than 3000 TSS were predicted, about 40% of which were estimated to be functional. This is the first systematic study of transcription initiation sites in a cyanobacterium.
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Affiliation(s)
- Jörg Vogel
- Department of Molecular Genetics and Biotechnology, Faculty of Medicine, Hebrew University, Jerusalem, Israel
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Fuller NJ, Marie D, Partensky F, Vaulot D, Post AF, Scanlan DJ. Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea. Appl Environ Microbiol 2003; 69:2430-43. [PMID: 12732508 PMCID: PMC154553 DOI: 10.1128/aem.69.5.2430-2443.2003] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phylogenetic relationships among members of the marine Synechococcus genus were determined following sequencing of the 16S ribosomal DNA (rDNA) from 31 novel cultured isolates from the Red Sea and several other oceanic environments. This revealed a large genetic diversity within the marine Synechococcus cluster consistent with earlier work but also identified three novel clades not previously recognized. Phylogenetic analyses showed one clade, containing halotolerant isolates lacking phycoerythrin (PE) and including strains capable, or not, of utilizing nitrate as the sole N source, which clustered within the MC-A (Synechococcus subcluster 5.1) lineage. Two copies of the 16S rRNA gene are present in marine Synechococcus genomes, and cloning and sequencing of these copies from Synechococcus sp. strain WH 7803 and genomic information from Synechococcus sp. strain WH 8102 reveal these to be identical. Based on the 16S rDNA sequence information, clade-specific oligonucleotides for the marine Synechococcus genus were designed and their specificity was optimized. Using dot blot hybridization technology, these probes were used to determine the in situ community structure of marine Synechococcus populations in the Red Sea at the time of a Synechococcus maximum during April 1999. A predominance of genotypes representative of a single clade was found, and these genotypes were common among strains isolated into culture. Conversely, strains lacking PE, which were also relatively easily isolated into culture, represented only a minor component of the Synechococcus population. Genotypes corresponding to well-studied laboratory strains also appeared to be poorly represented in this stratified water column in the Red Sea.
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Affiliation(s)
- Nicholas J Fuller
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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Abstract
During the twenty years or so since the discovery of tiny photosynthetic cells of the genus Synechococcus in marine oceanic systems, a tremendous expansion of interest has been seen in the literature pertaining to these organisms. The fact that they are ubiquitous and abundant in major oceanic regimes underlies their ecological importance as significant contributors to marine C fixation. Recent advances in the physiology and biochemistry of these organisms are presented here, focusing on strains of the MC-A and MC-B clusters; it is stressed that the data contained herein should be put into the context of the ecological niche occupied by particular genotypes in situ. This system is ripe for joining the often separate disciplines of molecular ecology and microbial physiology and provides a great opportunity to tease out the underlying processes that both mediate organism evolution and also the environmental factors that dictate this.
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Affiliation(s)
- David J Scanlan
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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Abstract
Recent data imply that for much of the Proterozoic Eon (2500 to 543 million years ago), Earth's oceans were moderately oxic at the surface and sulfidic at depth. Under these conditions, biologically important trace metals would have been scarce in most marine environments, potentially restricting the nitrogen cycle, affecting primary productivity, and limiting the ecological distribution of eukaryotic algae. Oceanic redox conditions and their bioinorganic consequences may thus help to explain observed patterns of Proterozoic evolution.
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Affiliation(s)
- A D Anbar
- Department of Earth and Environmental Sciences, University of Rochester, Rochester, NY 14627, USA.
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49
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Zehr JP, Ward BB. Nitrogen cycling in the ocean: new perspectives on processes and paradigms. Appl Environ Microbiol 2002; 68:1015-24. [PMID: 11872445 PMCID: PMC123768 DOI: 10.1128/aem.68.3.1015-1024.2002] [Citation(s) in RCA: 187] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Jonathan P Zehr
- Department of Ocean Sciences, Earth and Marine Sciences Building, Room A438, University of California, Santa Cruz, CA 95064, USA.
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50
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Lindell D, Post AF. Ecological aspects of ntcA gene expression and its use as an indicator of the nitrogen status of marine Synechococcus spp. Appl Environ Microbiol 2001; 67:3340-9. [PMID: 11472902 PMCID: PMC93026 DOI: 10.1128/aem.67.8.3340-3349.2001] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2001] [Accepted: 05/18/2001] [Indexed: 11/20/2022] Open
Abstract
Nitrogen nutrition in cyanobacteria is regulated by NtcA, a transcriptional activator that is subject to negative control by ammonium. Using Synechococcus sp. strain WH7803 as a model organism, we show that ntcA expression was induced when cells were exposed to nitrogen stress but not when they were subjected to phosphorus or iron deprivation. Transcript levels accumulated in cells grown on a variety of inorganic and organic nitrogen sources, with the sole exception of ammonium. ntcA transcription was induced when ammonium levels dropped below 1 microM and reached maximal levels within 2 h. Furthermore, the addition of more than 1 microM ammonium led to a rapid decline in ntcA mRNA. The negative effect of ammonium was prevented by the addition of L-methionine-D,L-sulfoximine (MSX) and azaserine, inhibitors of ammonium assimilation. Thus, basal ntcA transcript levels are indicative of ammonium utilization. Conversely, the highest ntcA transcript levels were found in cells lacking a nitrogen source capable of supporting growth. Therefore, maximal ntcA expression would indicate nitrogen deprivation. This state of nitrogen deprivation was induced by a 1-h incubation with MSX. The rapid response of ntcA gene expression to the addition of ammonium and MSX was used to design a protocol for assessing relative ntcA transcript levels in field populations of cyanobacteria, from which their nitrogen status can be inferred. ntcA was basally expressed in Synechococcus at a nutrient-enriched site at the northern tip of the Gulf of Aqaba, Red Sea. Therefore, these cyanobacteria were not nitrogen stressed, and their nitrogen requirements were met by regenerated nitrogen in the form of ammonium.
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Affiliation(s)
- D Lindell
- H. Steinitz Marine Biology Laboratory, Interuniversity Institute for Marine Sciences, Eilat 88103, Israel
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